(1) Background: Several studies have shown that active breaks have led to different improvements in their participants. However, no studies have assessed how they affect physical literacy (PL). (2) Aims: Therefore, this study will examine the effect of the PLBreaks programme on school children’s PL and body composition. (3) Methods: A parallel-group randomised controlled trial will be conducted with assessments of PL (Canadian Assessment of Physical Literacy Development) and body composition (height, bodyweight, fat mass and fat-free mass) before and after an active breaks programme. PLBreak programme will run for 3 months and will be carried out 3 days a week for 20 min each day. The PLBreaks programme will consist of two blocks of 10 min of different physical activities (PA). The first block will be focused on the acquisition of knowledge and healthy life habits that will contribute to the development of the domains of knowledge and understanding and daily activity. The second block will be focused on physical competence and motivation throughout games. (4) Conclusions: The present study will investigate the efficacy of PLBreaks in schoolchildren in improving their PL and body composition. If the efficacy of the program is demonstrated, including the programme in public education programmes can be possible. This could be a scientific breakthrough in terms of health-related PA improvement and adherence, as well as the prevention of diseases associated with inactivity.